Dear Feng Pan,
Thank you for your answer. I am sorry, I didn't notice earlier that
you had answered.
So, I've been following the instructions in AMBER manual, in the
section about ABMD where something about the 'UMBRELLA' mode is said.
My ncsu_abmd section in my MDIN file looks like:
***********************************
ncsu_abmd
mode = UMBRELLA
monitor_file = 'distances_out.dat'
monitor_freq =1
umbrella_file='free_energy_binary'
variable
type = DISTANCE
i=(272,273)
max = 2.0
end variable
variable
type = DISTANCE
i=(747,748)
max = 2.0
end variable
end ncsu_abmd
**********************************
I've explicited the variables I want to use as colective variable in
the way the AMBER manual explains. My umbrella_file is a binary file,
as you told me it should be. I've attached the ASCII version of the
umbrella_file, in case you could look it up at some point (it's pretty
simple: just three columns: first reaction coordinate, second one and
free energy; but still...)
After doing all of this and running the program, it immediately stops
with the following error:
** NCSU-Error ** : umbrella_load(filename='free_energy_binary') :
NetCDF: Unknown file format
And I have not been able to get around this.
Thank you for your help,
Diego Soler Polo
Quoting Feng Pan <fpan3.ncsu.edu>:
> Hi, Diego Soler Polo
>
> What you described can be realized in the new NFE (Non equilibrium Free
> energy ) module in Amber16.
>
> Basically you need to include the &abmd namelist and set the mode to
> UMBRELLA, and set the bias potential file.
> The module uses a binary file to store the bias potential, so you need to
> convert the ASCII data file to the binary file for input, but this is
> should be easy to do.
>
> you are read this updated manual for the details of this method
> http://ambermd.org/doc12/nfe.pdf
>
> you can give it a try on the conversion first, if you find any trouble you
> can send me the bias potential and I can help you. In the future, I may add
> the conversion to AmberTools so this is can be easily done.
>
> Furthermore, you can add a high-dimensional bias potential more than just
> one reaction coordinate by this method.
>
> Best
> Feng Pan
>
> On Fri, Nov 4, 2016 at 6:02 AM, <diego.soler.uam.es> wrote:
>
>> Hi,
>>
>> I would like to perform simulation with arbitrary bias potentials of
>> my choice. Let's say I have a particular reaction coordinate, Y, and
>> that I have a potential energy function V(Y) which I want to use as
>> bias potential.
>>
>> In practice, this bias potential would be described in a file
>> "bias_pot.dat" whose format would be as follows: N+1 columns, with N
>> the dimensionality of the reaction coordinate Y; N first columns
>> specifying values of the reaction coordinate along a certain grid with
>> which I discretize the possible values of Y; and the (N+1)th column to
>> specify the values of V(Y) in each row.
>>
>> Next, I would like to perform a MD simulation with the bias potential
>> specified in my file "bias_pot.dat". The idea would be that, at each
>> step of the MD simulation, the program would check the value of the
>> reaction coordinate, Y, and compute V by interpolation over the rows
>> of the file "bias_pot.dat"
>>
>> Is this possible in AMBER? I don't know if it is, but it would
>> certainly be great, because it would add a great deal of flexibility
>> for Umbrella simulations.
>>
>> Thanks,
>>
>> Diego Soler Polo, PhD student
>> Universidad Autónoma de Madrid
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Feng Pan
> Ph.D. Candidate
> North Carolina State University
> Department of Physics
> Email: fpan3.ncsu.edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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Received on Tue Nov 15 2016 - 03:00:03 PST
